Sorry it is a vacuum but I included implicit solvent in vdw parameters...So I need pbc as well.
On Wed, Sep 4, 2013 at 3:18 PM, Steven Neumann <s.neuman...@gmail.com>wrote: > Thank you. i am using my own vdw tables so need a cut off. > > > > > On Wed, Sep 4, 2013 at 3:13 PM, Justin Lemkul <jalem...@vt.edu> wrote: > >> >> >> On 9/4/13 10:11 AM, Steven Neumann wrote: >> >>> Thank you! Would you suggest just a cut-off for coulmb? >>> >>> >> Not a finite one. The best in vacuo settings are: >> >> pbc = no >> rlist = 0 >> rvdw = 0 >> rcoulomb = 0 >> nstlist = 0 >> vdwtype = cutoff >> coulombtype = cutoff >> >> -Justin >> >> On Wed, Sep 4, 2013 at 3:09 PM, Justin Lemkul <jalem...@vt.edu> wrote: >>> >>> >>>> >>>> On 9/4/13 10:03 AM, Steven Neumann wrote: >>>> >>>> DEa Users, >>>>> >>>>> My system involves protein in vacuum - 80 atoms in box of 9x9x9 nm3. I >>>>> want >>>>> to use PME in my mdp: >>>>> >>>>> rcoulomb = 2.0 >>>>> coulombtype = PME >>>>> pme_order = 4 >>>>> fourierspacing = 0.12 >>>>> >>>>> The cutoff needs to stay like this, I have my own tables with VDW, >>>>> bonds, >>>>> angles and dihedrals. >>>>> >>>>> i got the NOTE: >>>>> >>>>> The optimal PME mesh load for parallel simulations is below 0.5 >>>>> and for highly parallel simulations between 0.25 and 0.33, >>>>> for higher performance, increase the cut-off and the PME grid >>>>> spacing >>>>> >>>>> what setting would you suggest to use on 8 CPUs? >>>>> >>>>> >>>>> I would suggest not using PME :) The problem is PME is extremely >>>> inefficient in vacuo because it spends a lot of time doing nothing due >>>> to >>>> the empty space. Moreover, you're not likely really simulating in vacuo >>>> at >>>> that point because you've got PBC and therefore are really doing a >>>> simulation in more of a diffuse crystal environment, so there are >>>> probably >>>> artifacts. >>>> >>>> -Justin >>>> >>>> -- >>>> ==============================****==================== >>>> >>>> >>>> Justin A. Lemkul, Ph.D. >>>> Postdoctoral Fellow >>>> >>>> Department of Pharmaceutical Sciences >>>> School of Pharmacy >>>> Health Sciences Facility II, Room 601 >>>> University of Maryland, Baltimore >>>> 20 Penn St. >>>> Baltimore, MD 21201 >>>> >>>> jalemkul@outerbanks.umaryland.****edu <jalemkul@outerbanks.** >>>> umaryland.edu <jalem...@outerbanks.umaryland.edu>> | (410) >>>> 706-7441 >>>> >>>> ==============================****==================== >>>> >>>> -- >>>> gmx-users mailing list gmx-users@gromacs.org >>>> http://lists.gromacs.org/****mailman/listinfo/gmx-users<http://lists.gromacs.org/**mailman/listinfo/gmx-users> >>>> <htt**p://lists.gromacs.org/mailman/**listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>>> > >>>> * Please search the archive at http://www.gromacs.org/** >>>> Support/Mailing_Lists/Search<h**ttp://www.gromacs.org/Support/** >>>> Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>>before >>>> posting! >>>> >>>> * Please don't post (un)subscribe requests to the list. Use the www >>>> interface or send it to gmx-users-requ...@gromacs.org. >>>> * Can't post? Read >>>> http://www.gromacs.org/****Support/Mailing_Lists<http://www.gromacs.org/**Support/Mailing_Lists> >>>> <http://**www.gromacs.org/Support/**Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>>> > >>>> >>>> >> -- >> ==============================**==================== >> >> Justin A. Lemkul, Ph.D. >> Postdoctoral Fellow >> >> Department of Pharmaceutical Sciences >> School of Pharmacy >> Health Sciences Facility II, Room 601 >> University of Maryland, Baltimore >> 20 Penn St. >> Baltimore, MD 21201 >> >> jalemkul@outerbanks.umaryland.**edu <jalem...@outerbanks.umaryland.edu>| >> (410) >> 706-7441 >> >> ==============================**==================== >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> * Please search the archive at http://www.gromacs.org/** >> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before >> posting! >> * Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org. >> * Can't post? Read >> http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >> > > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
